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Fine-Scale Structure Analysis Shows Epidemic Patterns of Clonal Complex 95, a Cosmopolitan Escherichia coli Lineage Responsible for Extraintestinal Infection

The Escherichia coli lineage known as clonal complex 95 (CC95) is a cosmopolitan human-associated lineage responsible for a significant fraction of extraintestinal infections of humans. Whole-genome sequence data of 200 CC95 strains from various origins enabled determination of the CC95 pangenome. T...

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Autores principales: Gordon, David M., Geyik, Sarah, Clermont, Olivier, O’Brien, Claire L., Huang, Shiwei, Abayasekara, Charmalie, Rajesh, Ashwin, Kennedy, Karina, Collignon, Peter, Pavli, Paul, Rodriguez, Christophe, Johnston, Brian D., Johnson, James R., Decousser, Jean-Winoc, Denamur, Erick
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society for Microbiology 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451516/
https://www.ncbi.nlm.nih.gov/pubmed/28593194
http://dx.doi.org/10.1128/mSphere.00168-17
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author Gordon, David M.
Geyik, Sarah
Clermont, Olivier
O’Brien, Claire L.
Huang, Shiwei
Abayasekara, Charmalie
Rajesh, Ashwin
Kennedy, Karina
Collignon, Peter
Pavli, Paul
Rodriguez, Christophe
Johnston, Brian D.
Johnson, James R.
Decousser, Jean-Winoc
Denamur, Erick
author_facet Gordon, David M.
Geyik, Sarah
Clermont, Olivier
O’Brien, Claire L.
Huang, Shiwei
Abayasekara, Charmalie
Rajesh, Ashwin
Kennedy, Karina
Collignon, Peter
Pavli, Paul
Rodriguez, Christophe
Johnston, Brian D.
Johnson, James R.
Decousser, Jean-Winoc
Denamur, Erick
author_sort Gordon, David M.
collection PubMed
description The Escherichia coli lineage known as clonal complex 95 (CC95) is a cosmopolitan human-associated lineage responsible for a significant fraction of extraintestinal infections of humans. Whole-genome sequence data of 200 CC95 strains from various origins enabled determination of the CC95 pangenome. The pangenome analysis revealed that strains of the complex could be assigned to one of five subgroups that vary in their serotype, extraintestinal virulence, virulence gene content, and antibiotic resistance gene profile. A total of 511 CC95 strains isolated from humans living in France, Australia, and the United States were screened for their subgroup membership using a PCR-based method. The CC95 subgroups are nonrandomly distributed with respect to their geographic origin. The relative frequency of the subgroups was shown to change through time, although the nature of the changes varies with continent. Strains of the subgroups are also nonrandomly distributed with respect to source of isolation (blood, urine, or feces) and host sex. Collectively, the evidence indicates that although strains belonging to CC95 may be cosmopolitan, human movement patterns have been insufficient to homogenize the distribution of the CC95 subgroups. Rather, the manner in which CC95 strains evolve appears to vary both spatially and temporally. Although CC95 strains appeared globally as pandemic, fine-scale structure analysis shows epidemic patterns of the CC95 subgroups. Furthermore, the observation that the relative frequency of CC95 subgroups at a single locality has changed over time indicates that the relative fitness of the subgroups has changed. IMPORTANCE Escherichia coli clonal complex 95 represents a cosmopolitan, genetically diverse lineage, and the extensive substructure observed in this lineage is epidemiologically and clinically relevant. The frequency with which CC95 strains are responsible for extraintestinal infection appears to have been stable over the past 15 years. However, the different subgroups identified within this lineage have an epidemic structure depending on the host, sample, continent, and time. Thus, the evolution and spread of strains belonging to CC95 are very different from those of another cosmopolitan human-associated clonal complex, CC131, which has increased significantly in frequency as a cause of extraintestinal infection over the past 15 years due to the evolution and spread of two very closely related, nearly monomorphic lineages.
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spelling pubmed-54515162017-06-07 Fine-Scale Structure Analysis Shows Epidemic Patterns of Clonal Complex 95, a Cosmopolitan Escherichia coli Lineage Responsible for Extraintestinal Infection Gordon, David M. Geyik, Sarah Clermont, Olivier O’Brien, Claire L. Huang, Shiwei Abayasekara, Charmalie Rajesh, Ashwin Kennedy, Karina Collignon, Peter Pavli, Paul Rodriguez, Christophe Johnston, Brian D. Johnson, James R. Decousser, Jean-Winoc Denamur, Erick mSphere Research Article The Escherichia coli lineage known as clonal complex 95 (CC95) is a cosmopolitan human-associated lineage responsible for a significant fraction of extraintestinal infections of humans. Whole-genome sequence data of 200 CC95 strains from various origins enabled determination of the CC95 pangenome. The pangenome analysis revealed that strains of the complex could be assigned to one of five subgroups that vary in their serotype, extraintestinal virulence, virulence gene content, and antibiotic resistance gene profile. A total of 511 CC95 strains isolated from humans living in France, Australia, and the United States were screened for their subgroup membership using a PCR-based method. The CC95 subgroups are nonrandomly distributed with respect to their geographic origin. The relative frequency of the subgroups was shown to change through time, although the nature of the changes varies with continent. Strains of the subgroups are also nonrandomly distributed with respect to source of isolation (blood, urine, or feces) and host sex. Collectively, the evidence indicates that although strains belonging to CC95 may be cosmopolitan, human movement patterns have been insufficient to homogenize the distribution of the CC95 subgroups. Rather, the manner in which CC95 strains evolve appears to vary both spatially and temporally. Although CC95 strains appeared globally as pandemic, fine-scale structure analysis shows epidemic patterns of the CC95 subgroups. Furthermore, the observation that the relative frequency of CC95 subgroups at a single locality has changed over time indicates that the relative fitness of the subgroups has changed. IMPORTANCE Escherichia coli clonal complex 95 represents a cosmopolitan, genetically diverse lineage, and the extensive substructure observed in this lineage is epidemiologically and clinically relevant. The frequency with which CC95 strains are responsible for extraintestinal infection appears to have been stable over the past 15 years. However, the different subgroups identified within this lineage have an epidemic structure depending on the host, sample, continent, and time. Thus, the evolution and spread of strains belonging to CC95 are very different from those of another cosmopolitan human-associated clonal complex, CC131, which has increased significantly in frequency as a cause of extraintestinal infection over the past 15 years due to the evolution and spread of two very closely related, nearly monomorphic lineages. American Society for Microbiology 2017-05-31 /pmc/articles/PMC5451516/ /pubmed/28593194 http://dx.doi.org/10.1128/mSphere.00168-17 Text en Copyright © 2017 Gordon et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (http://creativecommons.org/licenses/by/4.0/) .
spellingShingle Research Article
Gordon, David M.
Geyik, Sarah
Clermont, Olivier
O’Brien, Claire L.
Huang, Shiwei
Abayasekara, Charmalie
Rajesh, Ashwin
Kennedy, Karina
Collignon, Peter
Pavli, Paul
Rodriguez, Christophe
Johnston, Brian D.
Johnson, James R.
Decousser, Jean-Winoc
Denamur, Erick
Fine-Scale Structure Analysis Shows Epidemic Patterns of Clonal Complex 95, a Cosmopolitan Escherichia coli Lineage Responsible for Extraintestinal Infection
title Fine-Scale Structure Analysis Shows Epidemic Patterns of Clonal Complex 95, a Cosmopolitan Escherichia coli Lineage Responsible for Extraintestinal Infection
title_full Fine-Scale Structure Analysis Shows Epidemic Patterns of Clonal Complex 95, a Cosmopolitan Escherichia coli Lineage Responsible for Extraintestinal Infection
title_fullStr Fine-Scale Structure Analysis Shows Epidemic Patterns of Clonal Complex 95, a Cosmopolitan Escherichia coli Lineage Responsible for Extraintestinal Infection
title_full_unstemmed Fine-Scale Structure Analysis Shows Epidemic Patterns of Clonal Complex 95, a Cosmopolitan Escherichia coli Lineage Responsible for Extraintestinal Infection
title_short Fine-Scale Structure Analysis Shows Epidemic Patterns of Clonal Complex 95, a Cosmopolitan Escherichia coli Lineage Responsible for Extraintestinal Infection
title_sort fine-scale structure analysis shows epidemic patterns of clonal complex 95, a cosmopolitan escherichia coli lineage responsible for extraintestinal infection
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451516/
https://www.ncbi.nlm.nih.gov/pubmed/28593194
http://dx.doi.org/10.1128/mSphere.00168-17
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